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Monday, December 27, 2010

FASEB is seeking nominations for its 2012 Excellence in Science Award, that recognizes the significant accomplishments of women scientists. We look forward to another list of nominees that reads like a 'Who's Who' of international science, containing the names of outstanding women in science who have accomplished scientific work of lasting impact and have contributed substantially to training the next generation of scientists. The 2012 season for the FASEB Excellence in Science Award will begin January 1, 2011.

Friday, December 17, 2010

Dear Colleagues, We are very happy to inform you that we have developed a new GUI for molecular modelling.Now this is online on Modeller\'s website http://salilab.org/modeller/wiki/Links with the link swift modeller. This is freely available to all.

MODELLER is command line argument based software which requires tedious formatting of inputs and writing of Python scripts which most people are not comfortable with. The visualization of output becomes cumbersome due to verbose files. This makes the whole software protocol very complex and requires extensive study of MODELLER manuals and tutorials. Here we describe SWIFT MODELLER, a GUI that automates formatting, scripting and data extraction processes and presents it in an interactive way making MODELLER much easier to use than before.

The screens in SWIFT MODELLER are designed keeping homology modeling in mind and their flow is a depiction of its steps. It eliminates the formatting of inputs, scripting processes and analysis of verbose output files through automation and makes pasting of the target sequence as the only prerequisite. It lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with

It would be great for me if you evaluate this tool and send the feedback, so that we can further improve this GUI. I am waiting for the suggestions, as these are very important for us.

Wednesday, December 15, 2010

Luciano brings expertise in health care and life science research to the Tetherless World Research Constellation

Joanne Sylvia Luciano has joined Rensselaer Polytechnic Institute as research associate professor in the Tetherless World Research Constellation. Luciano's research uses computational modeling and the World Wide Web to improve health care and advance medical discovery.

Luciano is an experienced technology consultant to major hospitals, biotechnology, and pharmaceutical companies. In addition to her nearly 30 years as a consultant, she held a joint appointment with Harvard Medical School and Massachusetts General Hospital for nine years, where she served as a lecturer and research scientist using computational modeling to study human disease.

She joins an interdisciplinary research team within the Tetherless World Research Constellation at Rensselaer, dedicated to advancing science and society through understanding and utilization of the World Wide Web.

"There's a vast amount of medically relevant data sitting in databases or websites and not being utilized," Luciano said. "The focus of my research is to create technologies that make it easy to do medical research whether you are a doctor, patient, pharmaceutical company, or searching for alternative therapies or lifestyle changes."

To accomplish these aims, Luciano utilizes ontologies and advanced mathematical modeling and computer simulation to understand illness, share medical data, and advance medical discovery and patient care. She builds computer-based technologies that improve healthcare by translating discoveries made at the laboratory or computer bench to the care received at an individual patient's bedside – known as bench to bedside care.

"There is an urgent need to shorten the time it takes to bring basic life science research results to clinical practice, and to get the clinical observations back to the research lab for further analysis," she said. "To do this, technologies need to be in place that allow scientists to better represent, reuse, and communicate medical data."

Luciano has helped develop several important ontologies including BioPAX, which is an international standard used for data related to cellular processes. BioPAX enables data to be combined in ways that were not possible before, making it possible to ask and answer complex biological questions. The language enables data to be combined automatically by computers, and because the representations are true to the current understanding of biology, other technology can be used to make inferences and reason over the data.

At the MITRE Corporation, she developed InfluenzO, an ontology to support influenza research, surveillance, and outbreak monitoring. She continues to lead this collaboration with the University of Maryland, the University of Texas Southwestern Medical Center, and the Canadian government.

She helped create the World Wide Web Consortium (W3C) Health Care and Life Sciences (HCLSIG) special interest group. The HCLSIG integrates the efforts of pharmaceutical and clinical researchers, doctors, and technologists to build the next generation of medical Web-based technology standards.

She is also a co-organizer of the BioPathways Consortium (BPC), a group of scientists working to support scientific advancement in the area of biological pathways. Such research, which has been a foundation of Luciano's career, uses computation to understand cell development, genetics, drug development, and disease.

In addition to ontologies, Luciano also utilizes mathematical modeling to study the dynamics of medical treatment response, looking for patterns that will help clinicians make more informed treatment choices. Patterns of treatment response often exist in groups of individuals. This study of treatment response patterns leads to so-called "personalized medicine" in which individual response to treatment can be modeled effectively and is important because individuals may respond differently to a treatment. She began this research at McLean Hospital while at Boston University, where she earned her doctorate. The work began as a study of different treatments (drug and therapy) for major depressive disorder (MDD).

That research led to the development of patented methods to select the best treatment for individual patients and predict the expected recovery patterns of treatments.

Luciano holds bachelor's and master's degrees in computer science and a doctorate incognitive and neural systems from Boston University.

About the Tetherless World Research Constellation

The Tetherless World Research Constellation at Rensselaer Polytechnic Institute (RPI) explores the research and engineering principles that underlie the Web, to enhance the Web's reach beyond the desktop and laptop computer, and develop new technologies and languages that expand the capabilities of the Web under three themes: Future Web, Informatics, and Semantic Foundations.

The goals of the constellation include making the next-generation Web natural to use while being responsive to the growing variety of policy, educational, societal, and scientific needs. Research areas include: Web science, privacy, intellectual property, general compliance, Web-based medical and health systems, semantic eScience, data-science, semantic data frameworks, next-generation virtual observatories, semantic data and knowledge integration, ontologies, semantic rules and queries, semantic applications, data and information visualization, and knowledge provenance, trust, and explanation for science.

The faculty, staff, and students (graduate and undergraduate) use powerful scientific and mathematical techniques from many disciplines to explore the modeling of the next-generation Web from network-, data-, and information-centric views.

Wednesday, December 8, 2010

Bioinformatics students, researchers and professionals may be interested in an online collection of scientific books that includes a growing number of titles related to the bioinformatics field.

The books are published by InTech, Open Access publisher of books and journals in science, technology and medicine, and are available on the reading platform www.intechopen.com. The full texts are absolutely free to read online, download in PDF format and share. No registration is required on the site.

The whole collection includes more than 270 books, and 30 new titles are due to come online by Christmas 2010. Books which may be of interest to the bioinformatics community include: